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Yorodumi- EMDB-49456: Cryo-EM structure of the Class 2 PI3K alpha/KRas complex on POPC/... -
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| Title | Cryo-EM structure of the Class 2 PI3K alpha/KRas complex on POPC/POPS nanodiscs | |||||||||
Map data | structure of the Class 2 PI3K alpha/KRas complex on POPC/POPS nanodiscs | |||||||||
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Keywords | lipid kinase / GTPase / ONCOPROTEIN / Transferase-Hydrolase complex | |||||||||
| Function / homology | Function and homology informationperinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / regulation of actin filament organization / negative regulation of actin filament depolymerization / phosphatidylinositol 3-kinase activator activity ...perinuclear endoplasmic reticulum membrane / regulation of toll-like receptor 4 signaling pathway / response to muscle inactivity / phosphatidylinositol kinase activity / phosphatidylinositol 3-kinase regulator activity / 1-phosphatidylinositol-3-kinase regulator activity / positive regulation of endoplasmic reticulum unfolded protein response / regulation of actin filament organization / negative regulation of actin filament depolymerization / phosphatidylinositol 3-kinase activator activity / response to butyrate / T follicular helper cell differentiation / IRS-mediated signalling / interleukin-18-mediated signaling pathway / phosphatidylinositol 3-kinase regulatory subunit binding / response to L-leucine / PI3K events in ERBB4 signaling / neurotrophin TRKA receptor binding / positive regulation of focal adhesion disassembly / cellular response to hydrostatic pressure / cis-Golgi network / Dengue Virus Attachment and Entry / Activated NTRK2 signals through PI3K / ErbB-3 class receptor binding / negative regulation of stress fiber assembly / transmembrane receptor protein tyrosine kinase adaptor activity / Activated NTRK3 signals through PI3K / phosphatidylinositol 3-kinase complex, class IB / phosphatidylinositol 3-kinase complex / TORC2 signaling / Co-stimulation by ICOS / RHOD GTPase cycle / positive regulation of protein localization to membrane / Signaling by cytosolic FGFR1 fusion mutants / vasculature development / Nephrin family interactions / RHOF GTPase cycle / kinase activator activity / Signaling by LTK in cancer / 1-phosphatidylinositol-4-phosphate 3-kinase activity / Signaling by LTK / anoikis / RND1 GTPase cycle / phosphatidylinositol 3-kinase complex, class IA / positive regulation of filopodium assembly / RND2 GTPase cycle / MET activates PI3K/AKT signaling / PI3K/AKT activation / relaxation of cardiac muscle / RND3 GTPase cycle / phosphatidylinositol-4,5-bisphosphate 3-kinase / 1-phosphatidylinositol-4,5-bisphosphate 3-kinase activity / growth hormone receptor signaling pathway / insulin binding / phosphatidylinositol 3-kinase / natural killer cell mediated cytotoxicity / phosphatidylinositol-3-phosphate biosynthetic process / Signaling by ALK / cardiac muscle cell contraction / RHOV GTPase cycle / 1-phosphatidylinositol-3-kinase activity / vascular endothelial growth factor signaling pathway / RHOB GTPase cycle / negative regulation of macroautophagy / GP1b-IX-V activation signalling / Erythropoietin activates Phosphoinositide-3-kinase (PI3K) / PI-3K cascade:FGFR3 / response to mineralocorticoid / response to dexamethasone / GMP binding / forebrain astrocyte development / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / positive regulation of protein kinase activity / LRR domain binding / negative regulation of epithelial cell differentiation / PI-3K cascade:FGFR1 / regulation of synaptic transmission, GABAergic / RHOJ GTPase cycle / RHOC GTPase cycle / response to isolation stress / phosphatidylinositol phosphate biosynthetic process / response to gravity / epithelial tube branching involved in lung morphogenesis / type I pneumocyte differentiation / Synthesis of PIPs at the plasma membrane / skeletal muscle cell differentiation / RHOU GTPase cycle / phosphatidylinositol-mediated signaling / Rac protein signal transduction / CDC42 GTPase cycle / RET signaling / negative regulation of anoikis / myoblast proliferation / Interleukin-3, Interleukin-5 and GM-CSF signaling / Signaling by RAS GAP mutants / Signaling by RAS GTPase mutants / Activation of RAS in B cells / T cell differentiation / PI3K events in ERBB2 signaling Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.23 Å | |||||||||
Authors | Torosyan H / Natalia J / Verba KA | |||||||||
| Funding support | United States, 1 items
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Citation | Journal: bioRxiv / Year: 2025Title: Structures of the PI3Kα/KRas complex on lipid bilayers reveal the molecular mechanism of PI3Kα activation. Authors: Hayarpi Torosyan / Michael D Paul / Allison Maker / Brigitte G Meyer / Natalia Jura / Kliment A Verba Abstract: PI3Kα is a potent oncogene that converts PIP2 to PIP3 at the plasma membrane upon activation by receptor tyrosine kinases and Ras GTPases. In the absence of any structures of activated PI3Kα, the ...PI3Kα is a potent oncogene that converts PIP2 to PIP3 at the plasma membrane upon activation by receptor tyrosine kinases and Ras GTPases. In the absence of any structures of activated PI3Kα, the molecular details of its activation remain unknown. Here, we present cryo-EM structures of the PI3Kα/KRas complex embedded in lipid nanodiscs, revealing a rich ensemble of PI3Kα states adopted at the membrane surface. The sequential addition of a lipid bilayer, PIP2 and an activating phosphopeptide leads to the progressive release of key inhibitory domains from the PI3Kα catalytic core, which directly correlates with the reorganization of its active site. While association with POPC/POPS nanodiscs partially relieves PI3Kα autoinhibition, incorporation of PIP2 triggers near-complete displacement of PI3Kα inhibitory domains and significant restructuring of active site regulatory motifs. The addition of the activating phosphopeptide induces dimerization of the PI3Kα/KRas complex through a p110α catalytic subunit-mediated interface that is sterically occluded in autoinhibited PI3Kα. In cells, this dimeric PI3Kα complex amplifies Akt signaling in response to growth factor stimulation. Collectively, our structures map the conformational landscape of PI3Kα activation and reveal previously unexplored interfaces for potential therapeutic targeting. | |||||||||
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_49456.map.gz | 176.3 MB | EMDB map data format | |
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| Header (meta data) | emd-49456-v30.xml emd-49456.xml | 23 KB 23 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_49456_fsc.xml | 14.9 KB | Display | FSC data file |
| Images | emd_49456.png | 41.8 KB | ||
| Masks | emd_49456_msk_1.map | 343 MB | Mask map | |
| Filedesc metadata | emd-49456.cif.gz | 7.7 KB | ||
| Others | emd_49456_half_map_1.map.gz emd_49456_half_map_2.map.gz | 318.8 MB 318.8 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-49456 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-49456 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9ni8MC ![]() 9ni3C ![]() 9ni4C ![]() 9ni5C ![]() 9ni6C ![]() 9ni7C ![]() 9nidC ![]() 9nieC ![]() 9nifC ![]() 9nlcC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_49456.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | structure of the Class 2 PI3K alpha/KRas complex on POPC/POPS nanodiscs | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 0.8189 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Mask #1
| File | emd_49456_msk_1.map | ||||||||||||
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| Density Histograms |
-Half map: Half Map B
| File | emd_49456_half_map_1.map | ||||||||||||
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| Annotation | Half Map B | ||||||||||||
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| Density Histograms |
-Half map: Half Map A
| File | emd_49456_half_map_2.map | ||||||||||||
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| Annotation | Half Map A | ||||||||||||
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| Density Histograms |
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Sample components
-Entire : full-length p85 alpha and p110 alpha heterodimer/KRas complex bou...
| Entire | Name: full-length p85 alpha and p110 alpha heterodimer/KRas complex bound to POPC/POPS/MSP1E3D1 nanodiscs |
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| Components |
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-Supramolecule #1: full-length p85 alpha and p110 alpha heterodimer/KRas complex bou...
| Supramolecule | Name: full-length p85 alpha and p110 alpha heterodimer/KRas complex bound to POPC/POPS/MSP1E3D1 nanodiscs type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3 |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 232.609 KDa |
-Macromolecule #1: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit ...
| Macromolecule | Name: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: phosphatidylinositol-4,5-bisphosphate 3-kinase |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 127.822578 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MSYYHHHHHH DYDIPTTENL YFQGAMGSMP PRPSSGELWG IHLMPPRILV ECLLPNGMIV TLECLREATL ITIKHELFKE ARKYPLHQL LQDESSYIFV SVTQEAEREE FFDETRRLCD LRLFQPFLKV IEPVGNREEK ILNREIGFAI GMPVCEFDMV K DPEVQDFR ...String: MSYYHHHHHH DYDIPTTENL YFQGAMGSMP PRPSSGELWG IHLMPPRILV ECLLPNGMIV TLECLREATL ITIKHELFKE ARKYPLHQL LQDESSYIFV SVTQEAEREE FFDETRRLCD LRLFQPFLKV IEPVGNREEK ILNREIGFAI GMPVCEFDMV K DPEVQDFR RNILNVCKEA VDLRDLNSPH SRAMYVYPPN VESSPELPKH IYNKLDKGQI IVVIWVIVSP NNDKQKYTLK IN HDCVPEQ VIAEAIRKKT RSMLLSSEQL KLCVLEYQGK YILKVCGCDE YFLEKYPLSQ YKYIRSCIML GRMPNLMLMA KES LYSQLP MDCFTMPSYS RRISTATPYM NGETSTKSLW VINSALRIKI LCATYVNVNI RDIDKIYVRT GIYHGGEPLC DNVN TQRVP CSNPRWNEWL NYDIYIPDLP RAARLCLSIC SVKGRKGAKE EHCPLAWGNI NLFDYTDTLV SGKMALNLWP VPHGL EDLL NPIGVTGSNP NKETPCLELE FDWFSSVVKF PDMSVIEEHA NWSVSREAGF SYSHAGLSNR LARDNELREN DKEQLK AIS TRDPLSEITE QEKDFLWSHR HYCVTIPEIL PKLLLSVKWN SRDEVAQMYC LVKDWPPIKP EQAMELLDCN YPDPMVR GF AVRCLEKYLT DDKLSQYLIQ LVQVLKYEQY LDNLLVRFLL KKALTNQRIG HFFFWHLKSE MHNKTVSQRF GLLLESYC R ACGMYLKHLN RQVEAMEKLI NLTDILKQEK KDETQKVQMK FLVEQMRRPD FMDALQGFLS PLNPAHQLGN LRLEECRIM SSAKRPLWLN WENPDIMSEL LFQNNEIIFK NGDDLRQDML TLQIIRIMEN IWQNQGLDLR MLPYGCLSIG DCVGLIEVVR NSHTIMQIQ CKGGLKGALQ FNSHTLHQWL KDKNKGEIYD AAIDLFTRSC AGYCVATFIL GIGDRHNSNI MVKDDGQLFH I DFGHFLDH KKKKFGYKRE RVPFVLTQDF LIVISKGAQE CTKTREFERF QEMCYKAYLA IRQHANLFIN LFSMMLGSGM PE LQSFDDI AYIRKTLALD KTEQEALEYF MKQMNDAHHG GWTTKMDWIF HTIKQHALN UniProtKB: Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform |
-Macromolecule #2: Phosphatidylinositol 3-kinase regulatory subunit alpha
| Macromolecule | Name: Phosphatidylinositol 3-kinase regulatory subunit alpha type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 83.710281 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MSAEGYQYRA LYDYKKEREE DIDLHLGDIL TVNKGSLVAL GFSDGQEARP EEIGWLNGYN ETTGERGDFP GTYVEYIGRK KISPPTPKP RPPRPLPVAP GSSKTEADVE QQALTLPDLA EQFAPPDIAP PLLIKLVEAI EKKGLECSTL YRTQSSSNLA E LRQLLDCD ...String: MSAEGYQYRA LYDYKKEREE DIDLHLGDIL TVNKGSLVAL GFSDGQEARP EEIGWLNGYN ETTGERGDFP GTYVEYIGRK KISPPTPKP RPPRPLPVAP GSSKTEADVE QQALTLPDLA EQFAPPDIAP PLLIKLVEAI EKKGLECSTL YRTQSSSNLA E LRQLLDCD TPSVDLEMID VHVLADAFKR YLLDLPNPVI PAAVYSEMIS LAPEVQSSEE YIQLLKKLIR SPSIPHQYWL TL QYLLKHF FKLSQTSSKN LLNARVLSEI FSPMLFRFSA ASSDNTENLI KVIEILISTE WNERQPAPAL PPKPPKPTTV ANN GMNNNM SLQDAEWYWG DISREEVNEK LRDTADGTFL VRDASTKMHG DYTLTLRKGG NNKLIKIFHR DGKYGFSDPL TFSS VVELI NHYRNESLAQ YNPKLDVKLL YPVSKYQQDQ VVKEDNIEAV GKKLHEYNTQ FQEKSREYDR LYEEYTRTSQ EIQMK RTAI EAFNETIKIF EEQCQTQERY SKEYIEKFKR EGNEKEIQRI MHNYDKLKSR ISEIIDSRRR LEEDLKKQAA EYREID KRM NSIKPDLIQL RKTRDQYLMW LTQKGVRQKK LNEWLGNENT EDQYSLVEDD EDLPHHDEKT WNVGSSNRNK AENLLRG KR DGTFLVRESS KQGCYACSVV VDGEVKHCVI NKTATGYGFA EPYNLYSSLK ELVLHYQHTS LVQHNDSLNV TLAYPVYA Q QRR UniProtKB: Phosphatidylinositol 3-kinase regulatory subunit alpha |
-Macromolecule #3: Isoform 2B of GTPase KRas
| Macromolecule | Name: Isoform 2B of GTPase KRas / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO / EC number: small monomeric GTPase |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 21.516656 KDa |
| Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
| Sequence | String: GMTEYKLVVV GAGGVGKSAL TIQLIQNHFV DEYDPTIEDS YRKQVVIDGE TCLLDILDTA GQEEYSAMRD QYMRTGEGFL CVFAINNTK SFEDIHHYRE QIKRVKDSED VPMVLVGNKC DLPSRTVDTK QAQDLARSYG IPFIETSAKT RQGVDDAFYT L VREIRKHK EKMSKDGKKK KKKSKTKCVI M UniProtKB: GTPase KRas |
-Macromolecule #4: tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanil...
| Macromolecule | Name: tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanilino]thieno[2,3-d]pyridazin-7-yl}phenyl]oxy}ethoxy)ethyl]carbamate type: ligand / ID: 4 / Number of copies: 1 / Formula: A1AZD |
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| Molecular weight | Theoretical: 581.658 Da |
-Macromolecule #5: MAGNESIUM ION
| Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: MG |
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| Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #6: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
| Macromolecule | Name: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER / type: ligand / ID: 6 / Number of copies: 1 / Formula: GNP |
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| Molecular weight | Theoretical: 522.196 Da |
| Chemical component information | ![]() ChemComp-GNP: |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 / Details: 50 mM Tris-HCL, 150 mM NaCl, 1mM TCEP |
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| Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GRAPHENE OXIDE / Support film - topology: HOLEY |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 5 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 47.7 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 105000 |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
United States, 1 items
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Processing
FIELD EMISSION GUN

